Help with exporting a 3d model in ~.stl format and adding colour data
According to wikipedia there are two different schemes in use for including color data in an stl file.  Unfortunately, they differ significantly from each other, and there is no way to specify which is in use in a file.  

So first, I would determine which format matlab exects.  This script says it can save in VisCam/SolidView format, so it would be reasonable to expect it to import this format as well, but you'd better check.  The problem here is that blender doesn't support the colored format, so you'll have to modify blender's export script...

Since all you're doing is exporting it to view with matlab, a different format that supports textures would probably be a better choice.  STL is meant for 3d prototyping, where color typically doesn't matter.

As for the other questions, I'm not sure.  Usually it's better to put each question in it's own post.